Magnesium in PDB 6qrv: X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy

All present enzymatic activity of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy:
5.3.1.5;

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy, PDB code: 6qrv was solved by H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.72 / 1.17
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	92.567, 97.577, 102.560, 90.00, 90.00, 90.00
R / Rfree (%)	10.4 / 12.4

The structure of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy also contains other interesting chemical elements:

Manganese	(Mn)	4 atoms
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy (pdb code 6qrv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy, PDB code: 6qrv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg416 b:9.9 occ:0.46 MN A:MN415 0.2 14.4 0.5 HO2 A:EDO401 1.5 18.1 1.0 OE1 A:GLU217 1.7 8.0 0.1 OE2 A:GLU181 2.0 13.0 1.0 OE1 A:GLU217 2.0 11.8 0.9 OD2 A:ASP245 2.0 13.3 1.0 OD2 A:ASP287 2.1 13.2 1.0 O2 A:EDO401 2.3 15.1 1.0 O A:HOH671 2.3 19.5 0.7 CD A:GLU217 2.9 7.9 0.1 CD A:GLU181 3.0 12.4 1.0 CG A:ASP287 3.1 11.0 1.0 CG A:ASP245 3.2 11.8 1.0 CD A:GLU217 3.3 10.0 0.9 OE1 A:GLU181 3.3 14.0 1.0 C2 A:EDO401 3.3 16.4 1.0 HB2 A:GLU217 3.4 10.1 0.9 HB3 A:ASP287 3.4 12.3 1.0 H22 A:EDO401 3.4 19.7 1.0 HB2 A:GLU217 3.5 9.5 0.1 HB2 A:ASP287 3.5 12.3 1.0 OE2 A:GLU217 3.6 8.0 0.1 H21 A:EDO401 3.6 19.7 1.0 CB A:ASP287 3.6 10.3 1.0 HE1 A:HIS220 3.6 12.0 0.7 HB3 A:ASP245 3.6 12.6 1.0 MN A:MN414 3.7 9.3 0.1 CB A:ASP245 3.9 10.5 1.0 HB2 A:ASP245 3.9 12.6 1.0 CG A:GLU217 3.9 7.8 0.1 HE1 A:HIS220 4.0 10.9 0.3 O A:HOH574 4.0 16.5 1.0 O A:HOH709 4.0 17.0 0.9 CG A:GLU217 4.1 9.2 0.9 CB A:GLU217 4.1 8.4 0.9 HG3 A:GLU217 4.1 9.4 0.1 CE1 A:HIS220 4.1 10.0 0.7 HG3 A:GLU217 4.1 11.1 0.9 CB A:GLU217 4.1 7.9 0.1 OE2 A:GLU217 4.2 10.3 0.9 OD1 A:ASP245 4.2 13.2 1.0 OD1 A:ASP287 4.2 11.1 1.0 CE1 A:HIS220 4.3 9.1 0.3 CG A:GLU181 4.3 11.6 1.0 O A:HOH727 4.4 77.7 0.9 HD21 A:ASN215 4.4 15.2 1.0 HB3 A:GLU217 4.4 10.1 0.9 NE2 A:HIS220 4.5 9.2 0.3 HG3 A:GLU181 4.5 13.9 1.0 HB3 A:GLU217 4.5 9.5 0.1 HG2 A:GLU181 4.5 13.9 1.0 HZ2 A:TRP16 4.6 13.2 1.0 HD22 A:ASN215 4.7 15.2 1.0 C1 A:EDO401 4.7 16.4 1.0 NE2 A:HIS220 4.7 10.3 0.7 HG2 A:GLU217 4.7 9.4 0.1 MN A:MN414 4.7 10.9 0.4 MN A:MN414 4.8 11.1 0.6 ND1 A:HIS220 4.8 9.5 0.7 H12 A:EDO401 4.8 19.7 1.0 ND2 A:ASN215 4.8 12.7 1.0 HO1 A:EDO409 4.8 72.5 1.0 HD1 A:HIS220 4.9 11.4 0.7 HG2 A:GLU217 4.9 11.1 0.9

Magnesium binding site 2 out of 2 in the X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Radiation Dose Series on Xylose Isomerase - 2.63 Mgy within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg417 b:18.7 occ:0.53 O A:HOH618 2.0 21.3 0.9 O A:HOH967 2.1 36.3 1.0 O A:HOH987 2.1 38.2 0.8 O A:HOH649 2.1 23.0 0.9 O A:HOH888 3.5 0.2 1.0 O A:HOH1001 3.9 59.0 0.9 O A:HOH774 4.0 25.6 0.9 H11 A:EDO406 4.1 65.6 1.0 OD2 A:ASP153 4.3 13.6 1.0 OD1 A:ASP153 4.3 14.3 1.0 O A:HOH955 4.3 79.2 1.0 CG A:ASP153 4.7 12.3 1.0 O A:HOH520 4.8 58.0 1.0 O A:HOH867 4.9 57.2 1.0 C1 A:EDO406 4.9 54.7 1.0 H21 A:EDO406 5.0 65.0 1.0

H.Taberman, C.S.Bury, M.J.Van Der Woerd, E.H.Snell, E.F.Garman. Structural Knowledge or X-Ray Damage? A Case Study on Xylose Isomerase Illustrating Both. J.Synchrotron Radiat. V. 26 931 2019.
ISSN: ESSN 1600-5775
PubMed: 31274415
DOI: 10.1107/S1600577519005599